I don't understand why the portion of the value attributable to the underlying land would factor into the structure size adjustment.
If you have a 1,000 SF home selling for $100 per SF ($100,000), and site value is 25,000, then the adjustment is going to be around $75 per SF. If cost new is $100 per SF then that means improvements are about 25% depreciated including physical, external, functional.
If you have a 1,000 SF home selling for $60 per SF ($60,000), and site value is $25,000, then the adjustment is going to be around $35. If cost new is $100 per SF then that means this improvement is about 65% depreciated including physical, external, functional.